DFT study of isomers of the ruthenium dihydride complex RuH<Subscript>2</Subscript>(CO)<Subscript>2</Subscript>(AsMe<Subscript>2</Subscript>Ph)<Subscript>2</Subscript>

A density functional theory (DFT) study of cct-As, ccc, and cct-CO isomers of the ruthenium dihydride complex RuH₂(CO)₂(AsMe₂Ph)₂ is reported (see Scheme for the labeling isomer 34 structures of RuH₂(CO)₂(AsMe₂Ph)₂). Complex geometries and relative energies of different isomers have been calculated with both B3LYP and M06-2X functionals. The results show that the B3LYP calculated Boltzmann populations of cct-As, ccc, and cct-CO isomers are 65.5, 34.2, and 0.3%, respectively. These are in better agreement with the experimental data than those calculated at the M06-2X level. However, the calculations of ¹H NMR chemical shifts were found to be better described with M06-2X than with B3LYP or with HF level of theories. In addition, a transition state between the two most stable isomers was determined through DFT/(B3LYP or M06-2X) calculations.

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Graphical Abstract Scheme: Labeling structure of RuH₂(CO)₂(AsMe₂Ph)₂

     

DFT study of CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.     

The effect of thermal treatment on antibacterial properties of nanostructured TiO<Subscript>2</Subscript>(N) films illuminated with visible light

This work focuses on the photocatalytic performances and antibacterial activity of nitrogen doped TiO₂ nanosystems with three and five layers obtained by a sol-gel route, followed by thermal treatment in oxygen or ammonia atmosphere at temperatures between 400 and 1000°C. Subsequently, the antibacterial activity of the obtained nanosystems on the Escherichia coli cells are determined and discussed. The obtained results show a significant dependence of the functional performances on the system’s composition. In particular, the antimicrobial activity of nitrogen-doped TiO₂ films is correlated with the temperature of thermal treatment and illumination time with visible artificial light.     

Photoinduced bactericidal activity of TiO<Subscript>2</Subscript> films

A decrease in CFU of gram-positive and gram-negative bacteria on the surface of UV illuminated TiO₂ films (wavelength of 380 nm) is shown. A 29, 45, and 47% decrease in bacterial viability of Staphylococcus aureus, Staphylococcus epidermidis, and Escherichia coli, respectively, was seen after 12-min exposition. It was first discovered that the reuse of TiO₂ films to test a bacterial suspension for viability removes UV-induced bactericidal activity. However, annealing of TiO₂ at a temperature above 400°C restores the photoinduced bactericidal activity to its initial state.     

Theoretical study of the reaction mechanism of CH<Subscript>3</Subscript>NO<Subscript>2</Subscript> with NO<Subscript>2</Subscript>, NO and CO: the bimolecular reactions that cannot be ignored

The intriguing decompositions of nitro-containing explosives have been attracting interest. While theoretical investigations have long been concentrated mainly on unimolecular decompositions, bimolecular reactions have received little theoretical attention. In this paper, we investigate theoretically the bimolecular reactions between nitromethane (CH₃NO₂)—the simplest nitro-containing explosive—and its decomposition products, such as NO₂, NO and CO, that are abundant during the decomposition process of CH₃NO₂. The structures and potential energy surface (PES) were explored at B3LYP/6-31G(d), B3P86/6-31G(d) and MP2/6-311?+?G(d,p) levels, and energies were refined using CCSD(T)/cc-pVTZ methods. Quantum chemistry calculations revealed that the title reactions possess small barriers that can be comparable to, or smaller than, that of the initial decomposition reactions of CH₃NO₂. Considering that their reactants are abundant in the decomposition process of CH₃NO₂, we consider bimolecular reactions also to be of great importance, and worthy of further investigation. Moreover, our calculations show that NO₂ can be oxidized by CH₃NO₂ to NO₃ radical, which confirms the conclusion reached formerly by Irikura and Johnson [(2006) J Phys Chem A 110:13974–13978] that NO₃ radical can be formed during the decomposition of nitramine explosives.     

A DFT study of addition reaction between fragment ion (CH<Subscript>2</Subscript>) units and fullerene (C<Subscript>60</Subscript>) molecule

The theoretical study of the interaction between CH₂ and fullerene (C₆₀) suggests the existence of an addition reaction mechanism; this feature is studied by applying an analysis of electronic properties. Several different effects are evident in this interaction as a consequence of the particular electronic transfer which occurs during the procedure. The addition or insertion of the methylene group results in a process, where the inclusion of CH₂ into a fullerene bond produces the formation of several geometric deformations. A simulation of these procedures was carried out, taking advantage of the dynamic semi-classical Born-Oppenheimer approximation. Dynamic aspects were analyzed at different speeds, for the interaction between the CH₂ group and the two bonds: CC (6, 6) and CC (6, 5) respectively on the fullerene (C₆₀) rings. All calculations which involved electrons employed DFT as well as exchange and functional correlation. The results indicate a tendency for the CH₂ fragment to attack the CC (6, 5) bond.     

Cellulose/carrageenan/TiO<Subscript>2</Subscript> nanocomposite for adsorption and photodegradation of cationic dye

Cellulose/carrageenan/TiO₂ nanocomposites were simply prepared by the co-dissolution of cellulose and carrageenan, and the dispersion of TiO₂ in 1-ethyl-3- methylimidazolium acetate, followed by reconstitution with anti-solvents. The cellulose/carrageenan/TiO₂ composite showed a much higher adsorption capacity for methylene blue (MB) than the cellulose and cellulose/TiO₂ composite. The cellulose/carrageenan/TiO₂ composite also degraded MB more efficiently in aqueous solution than the cellulose/ TiO₂ composite. The MB adsorption capacity of the cellulose/carrageenan/TiO₂ composite increased linearly with increasing carrageenan content in the composites.     

Interaction Between Nanoparticulate Anatase TiO<Subscript>2</Subscript> and Lactate Dehydrogenase

In order to study the mechanisms underlying the effects of TiO₂ nanoparticles on lactate dehydrogenase (LDH, EC1.1.1.27), Institute of Cancer Research region mice were injected with nanoparticulate anatase TiO₂ (5 nm) of various doses into the abdominal cavity daily for 14 days. We then examined LDH activity in vivo and in vitro and direct evident for interaction between nanoparticulate anatase TiO₂ and LDH using spectral methods. The results showed that nanoparticulate anatase TiO₂ could significantly activate LDH in vivo and in vitro; the kinetics constant (Km) and Vmax were 0.006 μM and 1,149 unit mg⁻¹ protein min⁻¹, respectively, at a low concentration of nanoparticulate anatase TiO₂, and 3.45 and 0.031 μM and 221 unit mg⁻¹ protein min⁻¹, respectively, at a high concentration of nanoparticulate anatase TiO₂. By fluorescence spectral assays, the nanoparticulate anatase TiO₂ was determined to be directly bound to LDH, and the binding constants of the binding site were 1.77 × 10⁸ L mol⁻¹ and 2.15 × 10⁷ L mol⁻¹, respectively, and the binding distance between nanoparticulate anatase TiO₂ and the Trp residue of LDH was 4.18 nm, and nanoparticulate anatase TiO₂ induced the protein unfolding. It was concluded that the binding of nanoparticulate anatase TiO₂ altered LDH structure and function.     

d(A)<Subscript>3</Subscript>d(T)<Subscript>3</Subscript> and d(G)<Subscript>3</Subscript>d(C)<Subscript>3</Subscript> B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics

We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)₃·d(T)₃ and d(G)₃·d(C)₃ nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra—molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)₃d(T)₃ and d(G)₃d(C)₃ duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.     

H<Subscript>2</Subscript>O<Subscript>2</Subscript>-induced acclimation of photosystem II to excess light is mediated by alternative respiratory pathway and salicylic acid

Acclimation to excess light is required for optimizing plant performance under natural environment. The present work showed that the treatment of Arabidopsis leaves with exogenous H₂O₂ can increase the acclimation of PSII to excess light. Treatments with H₂O₂ also enhanced the capacity of the mitochondrial alternative respiratory pathway and salicylic acid (SA) content. Our work also showed that the lack in alternative oxidase (AOX1a) in AtAOX1a antisense line and the SA deficiency in NahG (salicylate hydroxylase gene) transgenic mutant attenuated the H₂O₂-induced acclimation of PSII to excess light. It indicates that the H₂O₂-induced acclimation of PSII to excess light could be mediated by the alternative respiratory pathway and SA.     

TCNE-modified graphene as an adsorbent for N<Subscript>2</Subscript>O molecule: a DFT study

Adsorption behavior of nitrous oxide (N₂O) on pristine graphene (PG) and tetracyanoethylene (TCNE) modified PG surfaces is investigated using density functional theory. A number of initial adsorbate geometries are considered on both surfaces and the most stable ones are chosen upon calculation of the adsorption energies (E_ads). N₂O is found to adsorb in a weakly exoergic process (E_ads?～??3.18 kJ mol^?1) at the equilibrium distance of 3.52 Å on the PG surface. N₂O adsorption can be greatly enhanced with the presence of a TCNE molecule (E_ads?=??87.00 kJ mol^?1). Mulliken charge analysis confirms that adsorption of N₂O is not accompanied by distinct charge transfer from the surfaces to the molecule (? 0.001 │e│ for each case). Moreover, on the basis of calculated changes in the HOMO/LUMO energy gap, it is found that electronic properties of PG and TCNE modified PG are not sensitive toward adsorption of N₂O, indicating that both surfaces are not good enough to introduce as an N₂O detector. However, the considerable amount of E_ads in TCNE modified PG can be a guide to the design of graphene-based adsorbents for N₂O capture.     

Molecular properties of metal difluorides and their interactions with CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O molecules: a DFT investigation

A computational study of metal difluorides (MF₂; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca–F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn–Teller effect in nonlinear MF₂ molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO₂ with ScF₂ (Scc3 geometry) and TiF₂ (Tic2 geometry) caused CO₂ to shift from its usual linear geometry to a bent geometry (η²(C=O) binding mode), while it retained its linear geometry (η¹(O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H₂O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO₂. Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO₂ capture under moist conditions.

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Graphical abstract Interaction of metal difluorides with carbon dioxide and water

     

The influence of Sc doping on structural,electronic and optical properties of Be<Subscript>12</Subscript>O<Subscript>12</Subscript>, Mg<Subscript>12</Subscript>O<Subscript>12</Subscript> and Ca<Subscript>12</Subscript>O<Subscript>12</Subscript> nanocages: a DFT study

Density functional theory (DFT) calculations were used to study the effect of scandium doping on the structural, energetic, electronic, linear and nonlinear optical (NLO) properties of Be₁₂O₁₂, Mg₁₂O₁₂ and Ca₁₂O₁₂ nanoclusters. Scandium (Sc) doping on nanoclusters leads to narrowing of their E _g, which enhances their conductance greatly. Also, the polarizability (α) and first hyperpolarizability (β₀) of nanoclusters were dramatically increased as Be, Mg or Ca atoms are substituted with a Sc atom. Among all clusters, α and β₀ values for Sc-doped Ca₁₂O₁₂ were the largest. Consequently, the effect of the doping atom, as well as of cluster size, on electronic and optical properties was explored. Time dependent (TD)-DFT calculations were also carried out to confirm the β₀ values; the results show that the higher value of first hyperpolarizability belongs to Sc-doped Ca₁₂O₁₂, which has the smallest transition energy (ΔEgn). The results obtained show that these clusters can be candidates for using in electronic devices and NLO materials in industry.     

Improving Efficiency of TiO<Subscript>2</Subscript>:Ag /Si Solar Cell Prepared by Pulsed Laser Deposition

Titanium dioxide (TiO₂) has been extensively studied and demonstrated to be suitable to enhance the efficiency of solar cell. In this work, TiO₂ is doped with silver nanoparticles (AgNP’s) on glass and the Si substrate by using Pulsed Laser Deposition (PLD) technique. UV–vis spectroscopy, X-ray diffraction (XRD), X-ray fluorescence (XRF), Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), Atomic Force Microscope (AFM), electrical conductivity (σ _dc), Hall coefficient (R_H), current–voltage (I–V), and capacity–voltage (C–V) characterizations have been used to examine the optical, the morphological, and the electrical properties of the films. It has been found that 5 wt.% (Ag) doped TiO₂ thin film has the most effect on efficiency of TiO₂:Ag /Si solar cell. The (I–V) characteristics showed that the (TiO₂) thin film enhances the efficiency of the (p–n) junction solar cell from 1.26 % pure TiO₂ to 7.19 % with doping of noble metal (Ag) representing improvement in the efficiency of solar cell leading to estimate empirical equations between efficiency, extinction coefficient, and energy band gap which have a total fit with the experimental data.     

Theoretical study of structural patterns in CH<Subscript>2</Subscript>OP<Subscript>2</Subscript> isomers

DFT calculations have been performed on the derivatives of formula CH₂OP₂ to determine their total energy, the relative energy between the isomers and their geometry. Among compounds with a P-C-P linkage, the most stable one is the 2-hydroxy-1,2-diphosphirene II.1, a three-membered heterocycle with a P=C unsaturation. The phosphavinylidene(oxo)phosphorane HP=C=P(O)H IV.5 (which has the same skeleton as the experimentally obtained Mes*P=C=P(O)Mes*) lies 36.30 kcal mol^-1 above it. The least stable compounds are carbenes; the singlet carbenes are more stable than the triplet ones.     

H<Subscript>2</Subscript>O<Subscript>2</Subscript>-induced higher order chromatin degradation: A novel mechanism of oxidative genotoxicity

The genotoxicity of reactive oxygen species (ROS) is well established. The underlying mechanism involves oxidation of DNA by ROS. However, we have recently shown that hydrogen peroxide (H2O2), the major mediator of oxidative stress, can also cause genomic damage indirectly. Thus, H2O2 at pathologically relevant concentrations rapidly induces higher order chromatin degradation (HOCD), i.e. enzymatic excision of chromatin loops and their oligomers at matrix-attachment regions. The activation of endonuclease that catalyzes HOCD is a signalling event triggered specifically by H2O2. The activation is not mediated by an influx of calcium ions, but resting concentrations of intracellular calcium ions are required for the maintenance of the endonuclease in an active form. Although H2O2-induced HOCD can efficiently dismantle the genome leading to cell death, under sublethal oxidative stress conditions H2O2-induced HOCD may be the major source of somatic mutations.     

Self-assembly and photocatalytic activity of branched silicatein/silintaphin filaments decorated with silicatein-synthesized TiO<Subscript>2</Subscript> nanoparticles

The fundamental mechanisms of biomineralization and their translation into innovative synthetic approaches have yielded promising perspectives for the fabrication of biomimetic and bioinspired organic–inorganic hybrid materials. In siliceous sponges, the enzyme silicatein catalyzes the polycondensation of molecular precursors to nano-structured SiO₂ that is deposited on self-assembled filaments consisting of the two silicatein isoforms (silicatein-α and -β) and the scaffold protein silintaphin-1. Due to its broad substrate specificity silicatein is also able to convert in vitro various other precursors to non-biogenic materials (e.g., hydrolysis of titanium bis(ammonium lactato)-dihydroxide [TiBALDH] and subsequent polycondensation to titania [TiO₂]). In the present approach, silicatein was bioengineered to carry a protein tag (Arg-tag) that confers binding affinity to TiO₂. Then, by combining Arg-tagged silicatein-α with silicatein-β and silintaphin-1, self-assembled branched hybrid protein microfilaments were fabricated. Upon subsequent incubation with TiBALDH the filaments were decorated with TiO₂ and assayed for photocatalytic activity through photodegradation of the dye methylene blue. This is the first approach that considers concomitant application of two silicatein isoforms for the synthesis of bioinspired organic–inorganic hybrid materials. It is also the first time that the biocatalytic activity of the enzymes has been combined with both the structure-providing properties of silintaphin-1 and a TiO₂ affinity protein tag to fabricate self-assembled branched protein filaments as template for a silicatein-synthesized TiO₂ photocatalyst. The TiO₂-decorated filaments might be explored as a practical alternative to approaches where biotemplates have to be laboriously isolated from their original biological source prior to TiO₂ immobilization.     

Theoretical study of the novel sandwich compound [Au<Subscript>3</Subscript>Cl<Subscript>3</Subscript>Tr<Subscript>2</Subscript>]<Superscript>2+</Superscript>

A theoretical study of a sandwich compound with a metal monolayer sheet between two aromatic ligands is presented. A full geometry optimization of the [Au₃Cl₃Tr₂]²⁺ (1) compound, which is a triangular gold(I) monolayer sheet capped by chlorines and bounded to two cycloheptatrienyl (Tr) ligands was carried out using perturbation theory at the MP2 computational level and DFT. Compound (1) is in agreement with the 18–electron rule, the bonding nature in the complex may be interpreted from the donation interaction coming from the Tr rings to the Au array, and from the back-donation from the latter to the former. NICS calculations show a strong aromatic character in the gold monolayer sheet and Tr ligands; calculations done with HOMA, also report the same aromatic behavior on the cycloheptatrienyl fragments giving us an insight on the stability of (1). The Au –Au bond lengths indicate that an intramolecular aurophilic interaction among the Au(I) cations plays an important role in the bonding of the central metal sheet. Figure (a) Ground state geometry of complex 1; (b) Top view of compound 1 and Wiberg bond orders computed with the MP2/B1 computational method; (c) Lateral view of compound 1 and NICS values calculated with the MP2/B1 method; the values in parenthesis were obtained at the VWN/TZP level     

Bonding,aromaticity, and planar tetracoordinated carbon in Si<Subscript>2</Subscript>CH<Subscript>2</Subscript> and Ge<Subscript>2</Subscript>CH<Subscript>2</Subscript>

Natural bond orbital (NBO) analyses and dissected nucleus-independent chemical shifts (NICS _{π z z} ) were computed to evaluate the bonding (bond type, electron occupation, hybridization) and aromatic character of the three lowest-lying Si₂CH₂ (1-Si, 2-Si, 3-Si) and Ge₂CH₂ (1-Ge, 2-Ge, 3-Ge) isomers. While their carbon C₃H₂ analogs favor classical alkene, allene, and alkyne type bonding, these Si and Ge derivatives are more polarizable and can favor “highly electron delocalized”? and “non-classical”? structures. The lowest energy Si ₂CH₂ and Ge ₂CH₂ isomers, 1-Si and 1-Ge, exhibit two sets of 3–center 2–electron (3c-2e) bonding; a π-3c-2e bond involving the heavy atoms (C–Si–Si and C–Ge–Ge), and a σ-3c-2e bond (Si–H–Si, Ge–H–Ge). Both 3-Si and 3-Ge exhibit π and σ-3c-2e bonding involving a planar tetracoordinated carbon (ptC) center. Despite their highly electron delocalized nature, all of the Si₂CH₂ and Ge₂CH₂ isomers considered display only modest two π electron aromatic character (NICS(0) _{π z z} =--6.2 to –8.9 ppm, computed at the heavy atom ring center) compared to the cyclic-C ₃H₂ (–13.3 ppm).

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Graphical Abstract The three lowest Si2CH2 and Ge2CH2 isomers.

     

The adsorption of NO,NH<Subscript>3</Subscript>, N<Subscript>2</Subscript> on carbon surface: a density functional theory study

To explore the adsorption mechanism of NO, NH₃, N₂ on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N₂ physisorption, and N₂ is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH₃ physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface.

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Graphical abstract NH₃, N₂, NO adsortion on carbon surface